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Some Concepts of Graph Theory
Full text linkWe present some preliminary concepts of graph theory with interesting and easy examples
Strong and weak competitors can coexist in the same niche
Full text linkThe competitive exclusion principle postulates that two trophically identical but fitness different species can not stably coexist in the same niche. However, this principle contradicts the observed nature's species richness. This fact is known as the biodiversity paradox. Here, using a simple cellular automaton model, we mechanistically show how two trophically identical, but fitness different species may stably coexist in the same niche. As environment is stable and any trade-offs are absent in this model, it strongly violates the competitive exclusion principle
Role of cardiac resynchronization therapy in the development of new-onset atrial fibrillation: A single-center prospective study.
Full text linkAlbeit several studies examined the association between cardiac resynchronization therapy (CRT) and atrial fibrillation (AF) in heart failure (HF), results are still unclear and quite conflicting. We thereby designed a single-center prospective study to determine whether CRT has a favorable effect on the incidence of new-onset AF in a homogeneous population of patients with non-ischemic idiopathic dilated cardiomyopathy and severe heart failure HF. We enrolled 58 patients, AF naïve when received CRT. After 1 year of follow-up our population was subdivided into responders (72.4%) and non (27.6%), so to compare the incidence of AF after 1, 2 and 3 years of follow-up in these two groups. Already after 1 year, there is a significant (p<0.05) difference in new-onset AF in non-responder patients respect to responders (18.2% vs 3.3%). These data are confirmed at 2 year (33.3% vs 12.2%) and 3 year (50.0% vs 15.0%) follow-up. In particular, at 3 year follow-up, non-responders have an increased risk to develop new-onset AF (OR=5.67, 95% confidence interval = 1.36-23.59, p=0.019). The present work suggests a possible favorable role of this non-pharmacological therapy, on the prevention of AF
The Unfolded Protein Response and its potential role in Huntington's disease
Full text linkHuntington's disease (HD) is a progressive, neurodegenerative disease with fatal outcome. Although the disease-causing gene (huntingtin) has been known for some time, the exact cause of neuronal cell death is still unknown. One potential mechanism contributing to the massive loss of neurons in the brain of HD patients might be the unfolded protein response (UPR), which is activated by accumulation of misfolded proteins in the endoplasmatic reticulum (ER). As an adaptive response to counter-balance accumulation of un- or misfolded proteins, the UPR upregulates transcription of chaperones, temporarily attenuates new translation, and activates protein degradation via the proteasome. However, it is known that persistent ER stress and activated UPR can cause cell death by triggering of apoptosis. Nevertheless, the evidence linking UPR with HD progression remains inconclusive. Here, we present first analyses of UPR activation during HD based on available expression data. To elucidate the potential role of UPR as a disease-relevant process, we examine its connection to cell death and inflammatory processes. Due to the complexity of these molecular mechanisms, a systems biology approach was pursued
An albumin-derived peptide scaffold capable of binding and catalysis
Full text linkWe have identified a 101-amino-acid polypeptide derived from the sequence surrounding the IIA binding site of human albumin. The polypeptide contains residues that make contact with ligands as warfarin in the parent protein, and eight cysteine residues to form disulfide bridges, which stabilize the polypeptide structure. Seventy-four amino acids are located in six [alpha]-helical regions, with the remaining amino acids forming six connecting coil/loop regions. Codon usage optimization was used to express a GST fusion protein in E. coli in yields as high as 4 mg/l. This fusion protein retains its structural integrity and aldolase activity, the ability to direct the stereochemical outcome of a diketone reduction, and its binding capacity to warfarin and efavirenz. Notably, this newly cloned polypeptide represents a valuable starting point for the construction of libraries of binders and catalysts with improved proficiency
Mobile Image Ratiometry for the Detection of Botrytis cinerea (Gray Mold)
Full text linkMobile Platform Informatics (MPI) and Smartphone Informatics (SPI) methods like Mobile Image Ratiometry (MIR) are potentially transformative point-of-use instantaneous analysis tools that are useful across a variety of industries. In agriculture, MIR-compatible immuno test strips allow early detection of a number of biotic stressors before devastating crop losses occur. Here we describe a low-cost and easy-to-use Smartphone and/or tablet-based protocol (Mobile Assay Inc., www.mobileassay.com) for the detection and on-sight instantaneous analysis of B. cinerea, a fungus that causes significant damage to a variety of plants and flowers. Early detection and tracking of the B. cinerea fungus before the visible gray mold appears has the potential to increase agricultural productivity especially in the developing world
Ecological connection between fish preference in the diet of Siberian cranes and their incubation period in tundra zone
Full text linkWe researched the ecology of the third rarest crane species, Siberian crane, which breeds in northern-eastern Siberian tundra. Nesting in places near great lakes, this crane appears to be an indicator of the global warming processes that affect lake growth as a result of the permafrost situation close to the surface in tundra. Research has shown that these birds are presumably fish-eating during their incubation period, coinciding with the flooding season when fish come to areas around great lakes. Such a diet may be explained by the necessity of high-energy food during the incubating period as well as the particularity of this species for leaving plant resources around the nest point for the period of the first days after chick hatching. This situation emphasizes tight connections in the vulnerable northern ecosystems. If the water level in tundra lakes starts to be higher due to global warming, all these links may be destroyed
Recombination modulates how selection affects linked sites in Drosophila
Full text linkOne of the most influential observations in molecular evolution has been a strong association between regional recombination rate and amount of nucleotide polymorphism in those genomic regions, interpreted as evidence for ubiquitous natural selection. The alternative explanation, that recombination is mutagenic, has been rejected by the absence of a similar association between regional recombination rate and nucleotide divergence between species. However, many recent studies show that recombination rates are often very different even in closely related species, questioning whether an association between recombination rate and divergence between species has been tested satisfactorily. To circumvent this problem, we directly surveyed recombination across approximately 43% of the D. pseudoobscura physical genome in two separate recombination maps, and 31.3% of the D. miranda physical genome, and we identified both global and local differences in recombination rate between these two closely related species. Using only regions with conserved recombination rates between and within species and accounting for multiple covariates, our data support the conclusion that recombination is positively related to diversity because recombination modulates hitchhiking in the genome. Finally, our data show that diversity around nonsynonymous substitutions is recovered at closer distances in areas of higher recombination than in areas of lower recombination — empirically demonstrating that recombination rate can limit the size and severity of potential selective sweeps
Management and provision of computational models
Full text linkQuantitative models of biological systems provide an understanding of chemical and biological phenomena based on their underlying mechanisms. Moreover, they can be used for example, to predict the behaviour of a system under given conditions or direct future experiments. This has made quantitative models the perfect tools to answer a variety of questions in the biological sciences and has lead to a steady growth of the number of published models.

To maximise the benefits of this growing body of models, the field needs centralised model repositories that will encourage, facilitate and promote model dissemination and reuse. BioModels Database(http://www.ebi.ac.uk/biomodels/) has been developed to exactly fulfil those needs. In order to ensure the correctness of the models distributed, their structure and behaviour are thoroughly checked. To ease their understanding, the model elements are annotated with terms from controlled vocabularies as well as linked to relevant data resources. Finally, to allow their reuse, the models are provided encoded in community supported and standardised formats.

However, the modelling field is constantly evolving and data providers, like BioModels Database, are faced with new challenges. For example, models are getting more and more complex (with for instance the availability of whole organism metabolic network reconstructions) and this has a direct impact on the performance of hosting infrastructures and annotation procedures. Also, models are now being developed collaboratively: this requires new methodologies and systems, akin to the ones used in software development (with for example versioned repositories of models). Moreover, very different kinds of models are being developed by diverse communities, but ultimately their data management needs are very similar.

This talk will introduce the needs which lead to the development of BioModels Database, present the resource and its current infrastructure and finally discuss the challenges that we are facing today and the plans to overcome them
Near Infrared Reflectance Spectroscopy (NIRS) Determination of Isoflavone Contents for Selected Soybean Accessions
Full text linkSoybean isoflavones are of considerable interest in relation to their possible health effects in human diets. The rapid and economical determination of soybean isoflavone concentrations is essential for the investigation and development of soybean health foods as well as the selection of soybean seeds with optimal isoflavone levels for such foods. Fourier transforms near infrared reflectance spectroscopy (FT-NIRS) calibrations were developed for the rapid and cost-effective analysis of isoflavones in soybean seeds. FT-NIRS measurements were carried out in quadruplicate for 50 soybean lines selected from the USDA Soybean Germplasm Collection. The selected soybean seeds provided a wide range of isoflavone concentrations (from 0.3 to 6.0 mg/g) that is necessary for development of high-quality calibrations. Laboratory reference values of isoflavone composition were obtained by HPLC analysis of extracted soybean powders. Single soybean seeds were selected for each standard sample and were cut in half in order to avoid screening of the isoflavones NIR absorption bands by the seed coat. For comparison purposes, measurements were also made on soybean powders of the same samples. FT -NIR spectra were collected with a spectral range from 4000 to 12000 cm-1 at a resolution of 8 cm-1 on a Perkin-Elmer Spectrum one NTS spectrometer model. This spectrometer is optimized for high sensitivity analysis of single seed composition, being equipped with an NIRA, integrating sphere accessory and an extended range InGaAs detector